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Series GSE71279 Query DataSets for GSE71279
Status Public on Aug 12, 2016
Title Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions
Organisms Escherichia coli; Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Other
Summary We employ a massively parallel reporter assay (MPRA) to measure the ex vivo activities in K562 and HepG2 cells of more than 15,000 human candidate regulatory regions. The regulatory regions were tiled with overlapping constructs enabling high resolution computational inference of activating and repressive nucleotides.
 
Overall design Reporter mRNA-seq from HepG2 and K562 cells were transfected with a ~54,000-plex MPRA plasmid pool for a 'PilotDesign' and ~244,000-plex pool for a 'ScaleUpDesign'. In the 'PilotDesign' each regulatory region was associated with constructs at nine positions spaced in 30-bp increments with each position linked to 24 10-nt tags. In the 'ScaleUpDesign' each regulatory region was associated with constructs at 31 positions spaced in 5-bp increments with each position linked to a single 10-nt tag. There were two separate sets of sequences based on the 'ScaleUpDesign'. In the 'PilotDesign' all experiments were conducted with a SV40 promoter, while for the 'ScaleUpDesign' there were separate experiments based on a SV40 and minimal TATA promoter. The reporter mRNA tags facilitate quantitation of their abundances. The same tags were also sequenced from the transfected MPRA plasmid pool to facilitate normalization to plasmid copy numbers. All transfections were done in duplicate. MPRA plasmid pools were amplified and sequenced in replicate for the pilot design and for each design and promoter type for the 'ScaleUpDesign'.
 
Contributor(s) Ernst J, Melnikov A, Zhang X, Wang L, Rogov P, Mikkelsen TS, Kellis M
Citation(s) 27701403
Submission date Jul 23, 2015
Last update date May 15, 2019
Contact name Jason Ernst
E-mail(s) jason.ernst@ucla.edu
Organization name UCLA
Department Biological Chemistry
Street address 615 Charles E Young Dr South
City Los Angeles
State/province CA
ZIP/Postal code 90095
Country USA
 
Platforms (4)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL14548 Illumina HiSeq 2000 (Escherichia coli)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (26)
GSM1831757 HepG2_ScaleUpDesign1_minP_mRNA_Rep1
GSM1831758 HepG2_ScaleUpDesign1_minP_mRNA_Rep2
GSM1831759 HepG2_ScaleUpDesign1_SV40P_mRNA_Rep1
Relations
BioProject PRJNA290789
SRA SRP061466

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Supplementary file Size Download File type/resource
GSE71279_RAW.tar 82.5 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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